U.S. patent application number 16/094798 was filed with the patent office on 2019-05-16 for device for dna sample fragmentation.
The applicant listed for this patent is Etablissement Francais du Sang. Invention is credited to Mehdi ALIZADEH, Cyrus MAHDJOUBI.
Application Number | 20190143292 16/094798 |
Document ID | / |
Family ID | 56087430 |
Filed Date | 2019-05-16 |
United States Patent
Application |
20190143292 |
Kind Code |
A1 |
ALIZADEH; Mehdi ; et
al. |
May 16, 2019 |
DEVICE FOR DNA SAMPLE FRAGMENTATION
Abstract
The invention relates to a device for the fragmentation of DNA
samples that are in solution in a container, said device
comprising: --a vessel for receiving a liquid, the vessel being
provided with means for producing ultrasonic waves so as to spread
ultrasonic waves through the liquid; and --a first support element
resting on the vessel, the device being characterized in that it
further comprises a second support element having a passage
designed to receive the container, the second support element being
suspended by at least one suspension element forming at least one
swivel joint, such that a lower portion of the container can be
immersed in the liquid.
Inventors: |
ALIZADEH; Mehdi; (Rennes,
FR) ; MAHDJOUBI; Cyrus; (Queven, FR) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
Etablissement Francais du Sang |
LA PLAINE SAINT DENIS |
|
FR |
|
|
Family ID: |
56087430 |
Appl. No.: |
16/094798 |
Filed: |
June 19, 2017 |
PCT Filed: |
June 19, 2017 |
PCT NO: |
PCT/FR2017/051609 |
371 Date: |
January 28, 2019 |
Current U.S.
Class: |
536/23.1 |
Current CPC
Class: |
C12Q 1/6806 20130101;
C12Q 2523/301 20130101; B01F 11/0283 20130101; G01N 1/28 20130101;
B01J 19/10 20130101; B01L 9/06 20130101; B06B 3/00 20130101; C12Q
1/6806 20130101; C12Q 2523/301 20130101 |
International
Class: |
B01J 19/10 20060101
B01J019/10; C12Q 1/6806 20060101 C12Q001/6806; B01L 9/06 20060101
B01L009/06; B06B 3/00 20060101 B06B003/00; B01F 11/02 20060101
B01F011/02; G01N 1/28 20060101 G01N001/28 |
Foreign Application Data
Date |
Code |
Application Number |
Apr 19, 2016 |
FR |
1653466 |
Claims
1. A device for the fragmentation of DNA samples that are in
solution in a container, the device comprising: a vessel for
receiving a liquid, the vessel being provided with means for
producing ultrasonic waves so as to spread ultrasonic waves through
the liquid; and a first support element resting on the vessel, the
device further comprising a second support element comprising a
passage designed to receive the container, the second support
element being suspended from at least one suspension element at a
distance from said first support element by at least one suspension
element forming at least one swivel joint in such a way as to allow
for the immersion of a lower portion of the container in the
liquid.
2. The device according to claim 1, wherein the suspension element
is deformable.
3. The device according to claim 1 wherein the suspension element
comprises a means for adjusting arranged to modify the distance
between the first support element (4) and the second support
element.
4. The device according to claim 1, wherein the means for producing
ultrasonic waves comprises at least one ultrasonic transducer.
5. The device according to claim 4 wherein the means for producing
ultrasonic waves further comprises a signal generator arranged to
supply the transducer with an electric signal.
6. The device according to claim 5 wherein the signal generator
comprises a module for generating periodic signals.
7. The device according to claim 1 wherein the means for producing
ultrasonic waves is fastened onto an outer lower face of the
vessel.
8. The device according to claim 7 wherein the means for producing
ultrasonic waves is placed substantially vertically with the
passage of the second support element.
9. The device according to claim 1 wherein the first support
element comprises a passage in such a way as to allow a user to
access the passage of the second support element.
10. The device according to claim 1 wherein the second support
element is separate from the lateral faces of the vessel by a
predetermined distance in such a way as to limit the exposure of
the container to the edge effects in the vicinity of the lateral
faces created by the reflection of the ultrasonic waves by the
lateral faces.
Description
RELATED APPLICATIONS
[0001] The present application is a National Phase entry of PCT
Application No. PCT/FR2017/051609, filed Jun. 19, 2017, which
claims priority to FR 1653466, filed Apr. 19, 2016, the contents of
each being incorporated herein by reference in their
entireties.
TECHNICAL FIELD
[0002] The invention relates to the field of DNA fragmentation
which consists in obtaining, from a strand of DNA comprising a
large number of nucleotide bases, several portions of a strand
comprising a more restricted number of nucleotide bases. The
invention more particularly relates to a device for the
fragmentation of DNA samples.
BACKGROUND ART
[0003] Devices are known for the fragmentation of DNA samples, the
samples being in solution in a dedicated container. Such devices
conventionally comprise a vessel for receiving a liquid, the vessel
being provided with means for producing ultrasonic waves so as to
spread ultrasonic waves through the liquid; and a support element
resting on the vessel designed to receive the container. The means
for producing ultrasonic waves is designed to generate a field of
ultrasonic waves with predefined properties in a limited space of
the vessel. This characteristic limits the number of DNA samples
that it is possible to simultaneously fragment in the device. A
fragmentation process lasts on the average one minute. Currently,
the maximum number of fragmented samples simultaneously by such a
device is about eight. However, the samples are conventionally
stored in plates comprising a hundred wells in order to be able to
contain a hundred samples. In a perspective of productivity, it
would be interesting to simultaneously fragment all of the samples
of a plate.
[0004] Furthermore, the devices for the fragmentation of DNA
samples often impose the use of specific containers, in particular
when the container plays a role in the production or the
transmission of ultrasonic waves. This imposes a transfer of the
samples from an initial container to a specific container, which
constitutes a time-consuming manipulation. Moreover, these specific
containers represent an additional cost for the user.
SUMMARY
[0005] Embodiments of the invention propose a solution aiming to
overcome the aforementioned disadvantages while guaranteeing a
device that performs at least as well as what exists with a limited
production cost, in particular the duration of the fragmentation
process is maintained at about one minute and the homogeneity of
the length of the DNA strands obtained following the fragmentation
is equivalent to what exists. Embodiments of the invention propose
a solution that solves the technical problem of the creating of a
substantially homogenous ultrasonic field in a volume that contains
a large number of DNA samples without using a specific container.
An objective of embodiments of the invention is to allow for the
use of standard containers in the device for the fragmentation of
DNA samples and in particular the use of plates able to contain a
hundred samples, and even more, for the purpose of increasing the
productivity of such a device.
[0006] Embodiments of the invention relate to a device for the
fragmentation of DNA samples that are in solution in a container,
the device comprising a vessel for receiving a liquid, the vessel
being provided with means for producing ultrasonic waves so as to
spread ultrasonic waves through the liquid; and a first support
element resting on the vessel, the device being characterized in
that it further comprises a second support element comprising a
passage designed to receive the container, the second support
element being suspended from at least one suspension element at a
certain distance from said the first support element by at least
one suspension element forming at least one swivel joint in such a
way as to allow for the immersion of a lower portion of the
container in the liquid. The term swivel joint means a connection
that entirely connects two parts in translation but leaves them
free in rotation. Such a connection therefore comprises 3 degrees
of connections in translation and 3 degrees of freedom in rotation.
The suspension element forming a swivel joint makes it possible to
substantially attenuate the transmission of interfering ultrasonic
waves from the first support element to the second support element
thanks to a damping effect of the swivel joint. More generally, the
device is designed to inhibit as much as possible the transmission
of interfering ultrasonic waves to the container. Eliminating
interfering ultrasonic waves contributes to creating a field of
ultrasonic waves that is substantially homogeneous in the vicinity
of the container. Furthermore, the container is not imposed by the
device and varied shapes of the container are suitable. According
to an advantageous embodiment, the container is a plate comprising
a plurality of wells. Preferably, this plate is a standard plate
commonly used to transport and/or treat DNA samples.
[0007] According to a particular embodiment, the suspension element
is deformable in order to limit the propagation of the interfering
waves between the first support element and the second support
element.
[0008] According to a particular embodiment, the suspension element
comprises a means for adjusting arranged to modify the distance
between the first support element and the second support element.
The means for adjusting make it possible to adjust the
horizontality of the second support element and therefore of the
container and to adjust the position of the second support element
with respect to the bottom of the vessel and therefore the position
of the container with respect to the liquid.
[0009] According to a particular embodiment, the means for
producing ultrasonic waves comprises at least one ultrasonic
transducer transforming an electrical signal into a mechanical
signal. Preferably, the means for producing ultrasonic waves
comprise a plurality of transducers arranged according to a grid so
as to create a relatively homogeneous field of ultrasonic waves in
the vicinity of the container.
[0010] According to a particular embodiment, the means for
producing ultrasonic waves further comprises a signal generator
arranged to supply the transducer with an electric signal.
[0011] According to a particular embodiment, the signal generator
comprises a module for generating periodic signals. For example,
the signal generator comprises at least one piezoelectric
oscillator.
[0012] According to a particular embodiment, the signal generator
further comprises a signal amplifier that makes it possible to
amplify the signal generated by the module for generating periodic
signals before transmitting the signal to the transducer.
[0013] According to a particular embodiment, the signal generator
further comprises a frequency and/or phase scanning module in such
a way as to generate at least two signals having separate
frequencies and/or phases in a predetermined frequency band. The
frequency and/or phase scanning makes it possible to prevent the
appearance of fixed antinodes and nodes in stationary operation in
the presence of periodic waves.
[0014] According to a particular embodiment, the means for
producing ultrasonic waves is fastened onto an outer lower face of
the vessel. For example, the transducers are glued onto the bottom
of the vessel by means of an adhesive suitable for the transmission
of ultrasonic waves or are welded to the vessel. The means for
producing ultrasonic waves transmits the ultrasonic waves to the
lower face of the vessel, then the lower face of the vessel
transmits in turn the ultrasonic waves to the liquid.
[0015] According to a particular embodiment, when the device is in
operating position, the means for producing ultrasonic waves is
placed substantially vertically with the passage of the second
support element in such a way as to be centered with respect to the
passage. The vertical is defined as being the direction of the
force of gravity. The presence of the means for producing
ultrasonic waves at the vertical of the passage of the second
support element and therefore at the vertical of the container
contributes to creating a homogeneous field of ultrasonic waves in
the vicinity of the container via a symmetrical effect. However,
the symmetry is optional.
[0016] According to a particular embodiment, the device comprises a
second means for producing ultrasonic waves in order to actively
reduce, and even cancel, the interfering ultrasonic waves.
[0017] According to a particular embodiment, the first support
element comprises a passage in such a way as to allow a user to
access the passage of the second support element. The access to the
passage of the second support element makes it possible to place a
container in the second support element or to withdraw it
therefrom.
[0018] According to a particular embodiment, the suspension element
comprises at least three chains in swivel joint with the upper
plate and in swivel joint with the support. The three chains are
distributed in such a way as to make it possible to maintain the
second support element in a horizontal position while still
guaranteeing the degrees of mobility of a swivel joint. The
horizontality is defined as being perpendicular to the vertical
direction.
[0019] According to a particular embodiment, the second support
element is separate from the lateral faces of the vessel by a
predetermined distance, for example a distance of 10 centimeters,
in such a way as to limit the exposure of the container to the edge
effects in the vicinity of the lateral faces created by the
reflection of the ultrasonic waves by the lateral faces. This
characteristic contributes to the homogeneity of the field of
ultrasonic waves in the vicinity of the container.
[0020] According to a particular embodiment, the device further
comprises an outer frame wherein the vessel is placed. The frame
makes it possible to support the vessel and to isolate the outer
environments from the ultrasonic waves propagating in the
vessel.
[0021] According to a particular embodiment, the device comprises a
cover. The cover makes it possible to isolate the contents of the
vessel from the outside environment with a concern for safety and
hygiene.
[0022] According to a particular embodiment, the device further
comprises an overflow device intended to ensure the presence of a
predetermined level of liquid in the vessel. It is necessary that
the level of liquid by sufficiently high to immerse the portion of
the container comprising the DNA samples to be fragmented. However,
it is preferable that the second support element not be immersed in
order to prevent the edge effects linked to the reflection of the
ultrasonic waves on the second support element, which would be
detrimental to the homogeneity of the field of ultrasonic
waves.
[0023] According to a particular embodiment, the overflow device
comprises a drainage passage so as to remove an excess portion of
the liquid.
[0024] According to a particular embodiment, the device further
comprises a means for adjusting the horizontality of the vessel in
order to guarantee a homogeneous immersion of all of the wells of
the container in the liquid.
[0025] According to a particular embodiment, the means for
adjusting the horizontality of the vessel comprises adjustable
legs.
[0026] According to a particular embodiment, the means for
adjusting the horizontality of the vessel comprises a bubble spirit
level.
BRIEF DESCRIPTION OF THE DRAWINGS
[0027] Other innovative characteristics and advantages shall appear
in the description hereinafter, provided for the purposes of
information and in no way limiting, in reference to the accompany
drawings, wherein:
[0028] FIGS. 1a and 1b show a diagrammatical view and as a
cross-section of a device respectively according to a first and a
second embodiment of the invention;
[0029] FIG. 2 shows a diagrammatical view in perspective of the
device of FIG. 1a or of FIG. 1b; and
[0030] FIG. 3 shows a functional diagram of a means for producing
ultrasonic waves according to embodiments of the invention.
DETAILED DESCRIPTION
[0031] FIGS. 1a, 1b and 2 show a device 1 for the fragmentation of
DNA samples. The DNA samples to be fragmented are placed in
solution in a solution S and placed in a container C. For example,
the fragmentation device 1 makes it possible to obtain from a
genome comprising substantially 3 billion nucleotide bases, several
strand portions comprising substantially 400 bases. The solution S
used is typically water or an aqueous gel. The container C is
preferably a standard container, for example a plate comprising a
plurality of wells arranged according to a grid pattern, or a row
of test tubes.
[0032] The device 1 comprises a vessel 2, a means for producing
ultrasonic waves 3, a first support element 4, a second support
element 5, a suspension element 6, a frame 7, a cover 8 and a means
for adjusting the horizontality 9 of the vessel.
[0033] The vessel 2 is a sealed container designed to receive a
liquid L, typically water. The vessel 2 is advantageously made of
metal and more particularly of stainless steel so as to prevent the
oxidation of the vessel 2 in contact with water and to facilitate
the cleaning thereof with a concern for hygiene. The vessel 2 has
for example a parallelepiped shape and comprises a lower face and
four lateral faces. From a dimensional standpoint and purely for
the purposes of illustration, the lower face is substantially of
rectangular shape and its sides measure between 25 and 35
centimeters. The lateral faces have a vertical dimension of about
ten centimeters, with the vertical being defined by the direction
of the force of gravity.
[0034] The vessel 2 is placed in the frame 7. The frame is a
container able to insulate the outside environment from the
ultrasonic waves propagating in the vessel 2. The frame 7 is
advantageously made of metal and more particularly of stainless
steel. The frame 7 has for example a parallelepiped shape and
comprises a lower face and four lateral faces. From a dimensional
standpoint and purely for the purposes of illustration, the lower
face is substantially of rectangular shape and its sides measure
about forty centimeters. The lateral faces have a vertical
dimension of about twenty centimeters.
[0035] The lateral faces of the vessel 2 comprise upper edges
resting on the lateral faces of the frame 7 in such a way that a
space is present between the outer lower face of the vessel 2 and
the inner lower face of the frame 7. Advantageously, the interfaces
between the upper edges of the vessel 2 and the lateral faces of
the frame 7 comprise joints 10 that limit the propagation of
interfering waves between the vessel 2 and the frame 7.
[0036] The first support element 4 has for example substantially
the shape of a plate comprising edges. From a dimensional
standpoint and purely for the purposes of illustration, the plate
is substantially of rectangular shape and its sides measure between
25 and 35 centimeters. The first support element 4 is removably
nested on the edges of the lateral faces of the vessel in such a
way as to guarantee a substantially fixed position of the first
support element 4 in relation to the vessel 2. Advantageously, the
nesting of the first support element 4 with the vessel has a
clearance for example filled with damping joints 10 that limit the
propagation of interfering waves between the vessel 2 and the first
support element 4. The first support element 4 comprises a passage
40 substantially at its center. From a dimensional standpoint and
purely for the purposes of illustration, the passage 40 is
substantially of rectangular shape and its sides measure about
fifteen centimeters. The first support element 4 is advantageously
made of metal and more particularly of stainless steel so as to
prevent the oxidation thereof in contact with water and to
facilitate the cleaning thereof. The first support element 4
comprises advantageously handles 41 that facilitate the handling
thereof. For example, the handles 41 are sets of two passages in
the first support element arranged to make it possible to grasp the
first support element by respectively inserting two fingers into
the passages in such a way as to pinch the first support element
4.
[0037] The second support element 5 has substantially for example a
plate shape. From a dimensional standpoint and purely for the
purposes of illustration, the plate is substantially of rectangular
shape and its sides measure about fifteen centimeters. The second
support element 5 comprises a passage 50 substantially at its
center. From a dimensional standpoint and purely for the purposes
of illustration, the passage 50 is substantially of rectangular
shape and its sides measure about ten centimeters. The second
support element 5 is advantageously made of metal and more
particularly of stainless steel so as to prevent the oxidation
thereof in contact with water and to facilitate the cleaning
thereof.
[0038] The second support element 5 is suspended from the first
support element 4 by the suspension element 6 forming a swivel
joint. The suspension element 6 advantageously comprises 4 chains
61 respectively connecting four points of the support element 4, in
the vicinity of the four corners of the passage 40, to four points
of the support element 5, in the vicinity of the four corners of
the support 5. Each chain 61 comprises two ends, the first end
being as a swivel joint with the first support element 4 and the
second end being as a swivel joint with the second support element
5. According to other embodiments, the chains 61 are replaced with
rods, rings or cords. Such suspension elements 6 that can be
deformed extend between the first support element 4 and the second
support element 5 according to a length for example of about 4
centimeters and make it possible to maintain the second support
element substantially at the center of the vessel in horizontal
position, the horizontal being defined as being perpendicular to
the vertical, while still limiting the transmission of ultrasonic
waves through the suspension element 6 thanks to the damping nature
conferred by the swivel joint.
[0039] According to a particular embodiment shown in FIG. 1b, the
suspension element 6 comprises a means for adjusting arranged to
modify the distance between the first support element 4 and the
second support element 5. The means for adjusting comprise two
cross members 63 substantially perpendicular to the chains 61 and
four screws 62 connecting the first support element 4 to the cross
members 63. By screwing or unscrewing the screws 62, the distance
between the first support element 4 and the cross members 63 is
modified. Advantageously, the four screws 62 are inserted into the
first support element 4 respectively at four points of the support
element 4 in the vicinity of the four corners of the passage 40.
Two adjacent screws are respectively screwed in the two ends of a
first cross member, the other screws are respectively screwed in
the two ends of the second cross member. Four corners of the second
support element 5 in the vicinity of the four corners of the
support element 5 are respectively connected to the four ends of
the two cross members by chains 61 substantially in the extension
of the screws 62.
[0040] The second support element 5 is intended to receive a
container C, typically a plate comprising a plurality of wells to
receive DNA samples. The container C is placed in such a way that
the wells are in the passage 50 and that the direction according to
which the wells extend is vertical, with the ends of the container,
at the periphery of the wells, resting on the second support
element 5.
[0041] The second support element 5 is separate from the lateral
faces of the vessel by a predetermined distance, for example a
distance of 10 centimeters, in such a way as to limit the exposure
of the container C to the edge effects in the vicinity of the
lateral faces created by the reflection of the ultrasonic waves by
the lateral faces.
[0042] The vessel 2 is filled with liquid L so as to immerse the
distal end of the wells and to leave the second support element 5
in the open air so as to prevent the reflection of the ultrasonic
waves propagating in the liquid L by the support element 5. The
vessel 2 comprises for example between 5 and 7 centimeters of
liquid L. During the filling operation of the vessel 2, the first
and the second support elements are removed from the vessel 2 in
such a way as to pour the liquid L into the vessel 2. The level of
liquid L is predefined and must be accurate to the nearest
millimeter. In order to precisely control the level of liquid L in
the vessel 2, the vessel 2 comprises an overflow device 21.
According to the embodiment shown, the overflow mechanism comprises
a drainage passage 210 in a lateral face of the vessel at a height
corresponding to the desired level of liquid. The excess liquid is
removed by a conduit 211. The conduit 211 conveys the excess liquid
to the outside of the frame 7 through a passage in the frame 7.
According to an embodiment not shown, the excess liquid is
collected in a container fastened to the frame 7. According to
another embodiment not shown, the overflow device 21 comprises a
wall that delimits a sealed compartment in the vessel 2, the wall
being arranged so that the excess liquid passes over an upper edge
of the wall.
[0043] The cover 8 covers the frame 7 and makes it possible to
isolate the contents of the vessel 2 from the outside environment
with a concern for safety and hygiene. Advantageously, the cover 8
comprises joints 10 at the interfaces between the cover 8 and the
first support element 4 or between the cover 8 and the vessel 2 in
such a way as to limit the propagation of the interfering waves on
these interfaces.
[0044] The means for adjusting the horizontality 9 of the vessel
comprises adjustable legs 91 and a bubble spirit level 92. In the
embodiment shown, the adjustable legs 91 and the bubble spirit
level 92 are fastened onto the outer lower face of the frame 7.
[0045] The means for producing ultrasonic waves 3 comprises a
plurality of transducers 31, for example 6 transducers arranged
according to a grid comprising 2 lines of 3 transducers in order to
create a relatively homogeneous field of ultrasonic waves in the
vicinity of the container C. The transducers transform an electric
signal into a mechanical signal generating ultrasonic waves. The
transducers are fixed to an outer face of the vessel 2, for example
they are glued by means of an adhesive suitable for the
transmission of ultrasonic waves or they are welded.
Advantageously, the transducers are fastened onto an outer lower
face of the vessel, vertical with the passage 50 of the second
support element 5.
[0046] FIG. 3 shows a means for producing ultrasonic waves 3. The
transducers 31 are supplied with an electrical signal by a signal
generator 32. Advantageously, the signal generator 32 comprises a
module for generating periodic signals 322, for example a
piezoelectric oscillator, and a signal conditioning and power
electronic module 321 that amplifies the signal generated by the
module for generating periodic signals 322. Advantageously, in
order to create a substantially homogenous field of ultrasonic
waves in the vicinity of the container and, in particular, so as to
prevent the appearance of antinodes and nodes in stationary
operation, the signal generator 32 comprises a frequency scanning
module 323 in such a way as to generate at least two signals having
separate frequencies in a predetermined frequency band, for example
a frequency band between 24 kHz and 28 kHz. Advantageously, the
signal generator 32 further comprises a module for regulating the
modulation in amplitude and in phase so as to be able to vary the
amplitude and the phase of the signals generated still with the
objective of preventing the appearance of antinodes and nodes.
[0047] Embodiments of the invention are described hereinabove as
examples. It is understood that those skilled in the art are able
to carry out different alternative embodiments of the invention, by
associating for example the various characteristics hereinabove
taken independently or in combination, without however leaving the
scope of the invention.
* * * * *